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Escaping the matrix: a new algorithm for phylogenetic comparative studies of co-evolution.

Maggie Wojcicki1, Daniel R Brooks

  • 1Department of Zoology, University of Toronto, 25 Harbord Street, Toronto, ON, M5S 3G5, Canada.

Cladistics : the International Journal of the Willi Hennig Society
|December 11, 2021
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Summary

A new algorithm, Phylogenetic Analysis for Comparing Trees (PACT), generates host cladograms from parasite phylogenies. PACT ensures co-evolutionary analyses are consistent with all parasite-host data, accounting for complex evolutionary events.

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Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Phylogenetics

Background:

  • Reconstructing host evolutionary relationships from parasite phylogenies is crucial for understanding co-evolution.
  • Existing methods may not fully utilize all available parasite-host data or account for complex evolutionary scenarios.

Purpose of the Study:

  • To introduce and describe the Phylogenetic Analysis for Comparing Trees (PACT) algorithm.
  • To develop a method for generating host cladograms that are logically consistent with parasite phylogenies and parasite-host cladograms.

Main Methods:

  • PACT algorithm development based on parasite-host cladograms.
  • Incorporation of co-speciation, host switching, host range expansion, reticulated evolution, and extinction events.
  • Ensuring all data from input cladograms is used without a priori weighting or post-hoc manipulation.

Main Results:

  • PACT generates host cladograms that satisfy "Assumption 0": complete data utilization and logical consistency.
  • The algorithm successfully accounts for diverse evolutionary events including host switching and reticulations.
  • Demonstrates a robust method for co-evolutionary analysis without data manipulation.

Conclusions:

  • PACT provides a comprehensive framework for inferring host evolutionary history from parasite phylogenies.
  • The algorithm enhances the accuracy and completeness of co-evolutionary studies.
  • PACT offers a valuable tool for researchers investigating host-parasite dynamics and evolutionary congruence.